On 29/12/2010 6:33 PM, delara aghaie wrote:
Dear Justin
many thanks for your email and your comments.
I found aminoacids.dat in the following pat
*/apps/gromacs/4.0.5/share/gromacs/top*
I connect to imerial college via vpn. they have installed several
gromacs versions.
I only write
*module load mpi* and then
*module load gromacs*
and then the gromacs commands become active.
These module files should be setting your paths correctly. You should
also be able to choose different GROMACS versions if such are installed.
Please consult the documentation for how the site uses modules, or ask
the sysadmins.
-------
the g_msd_mpi command worked and now I have msd.xvg file and I plotted
it using gnuplot with this command:
gnuplot "msd.xvg" u 1:2 w l
now pls let me know how can I save this plot? I have written about
that but I am confused.
Note that this is a gnuplot question, not a GROMACS question. There are
various ways to "save" a gnuplot plot, and the best approach varies with
what you want to do next. Please have a look at some gnuplot tutorial or
documentation material for information here.
Mark
Thanks for your time
Best regards
Delara
*
*
--- On *Wed, 12/22/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] location of aminoacids.dat
To: "Gromacs Users' List" <gmx-users@gromacs.org>
Date: Wednesday, December 22, 2010, 5:00 PM
First, please start a new thread if you are asking a new
question. Hijacking an existing thread confuses the archive and
will likely get your question ignored by anyone not interested in
reading about Buckingham potentials. I have changed the subject
line appropriately.
See comments below.
delara aghaie wrote:
> Dear Justin
> I hope all is well with you. I have faced a problem. I connect
to imperial college london from my conunty to do the simulations.
Today I faced an strange problem.
> every command wich I want to use for ex: g_msd_mpi or make_ndx_mpi
> I get this fatal error:
> *Fatal error:
> Library file aminoacids.dat not found in current dir nor in
default directories.
> (You can set the directories to search with the GMXLIB path
variable)*
> It is strange because my system is DPPC monolayer and does not
have nothing to do with proteins !!!
>
That doesn't matter. Certain input files are required by certain
Gromacs tools. In all likelihood, you simply haven't set up your
environment properly, but I'm not sure how that's possible.
What version of Gromacs are you using? How was it installed? Are
the Gromacs executables included in your $PATH, or do you have to
find them manually in order to use them (i.e., do you run
/path/to/gromacs/bin/grompp or just grompp)?
Also note that there is no value in compiling the entire Gromacs
suite with an MPI compiler. I've seen that cause weird behavior
before, but I doubt it's necessarily related here. The only
MPI-aware program is mdrun.
-Justin
> your help would be greatly appreciated/
> *Best regards*
> *Delara*
> *
> *
>
> --- On *Wed, 12/22/10, Justin A. Lemkul /<jalem...@vt.edu
<http://us.mc1301.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/*
wrote:
>
>
> From: Justin A. Lemkul <jalem...@vt.edu
<http://us.mc1301.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
> Subject: Re: [gmx-users] buckingham potentials
> To: "Gromacs Users' List" <gmx-users@gromacs.org
<http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
> Date: Wednesday, December 22, 2010, 8:04 AM
>
>
>
> sreelakshmi ramesh wrote:
> > Dear justin,
> > I have no clues about rewriting a force field
> so i think i can t proceed with this anymore.
> >
> > thanks a lot for your patient reply.
>
> For the future, you will waste a lot less time (your own,
and that
> of those who are trying to help you) if you provide a clear,
concise
> statement of what you hope to accomplish in your very first
post. You began this adventure seeking help on how to
(generically) use
> Buckingham potentials. What you should have asked was how
to use
> Buckingham potentials within the Gromos force field. Then,
instead
> of swapping ten emails, you would have received your answer
in one.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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